Transcriptome analysis has enhanced our understanding of the molecular constituents of cells and tissues. Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy.
Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. We used ROC, Matthew’s correlation coefficient and RMSD to determine the overall performance characteristics. Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson’s r = 0.92) and Ion Torrent Proton (Pearson’s r = 0.92). We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton).
The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis.
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